In my experience, bots do not work correctly with siege. Because of that, a siege map will never rotate until real players join and play the map. The server will sit perpetually empty on the same map until then. Incidentally, allowing map votes will also break a custom map rotation. Just a few weaknesses of this game server.

Also, the restart of the map to switch teams is considered a map restart (like rounds on a Duel server) so it is tricky to make a change in gametype in a rotation with with the Duel, Power Duel, or Siege gametypes. Same thing happens if g_dowarmup is "1" and is working on the mod (it doesn't in basejka). Warmup has to be disabled in the line preceeding the line with a change in gametype.

Where did you get bots that play siege correctly including joining the game and playing before real players enter so that the map rotation does not stall out? How do you have it set up that map voting won't break the custom rotation? I'm interested in both if they work.

In terms of the gametype being set before or after the map changes, as long as you put all of your settings BEFORE the map command, they will take effect prior to the map change and will be applied to that map. So what razorace has does work fine because it sets the gametype going into the map change, not after.